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Core commits
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Recent Commits to bioperl-live:master

Merge pull request #101 from christiam/master
Merge pull request #104 from douglasgscofield/master
Merge pull request #111 from adsj/master
Accept space after equal sign in qualifiers when reading EMBL.
merge upstream
Need to move the Deobfuscator to a separate directory, as this collides
modify RTD URL to point to a common spot, will add docs as subprojects when possible
add readthedocs badge; will gradually start migrating docs to that site (including HOWTOs, installation etc)
even better DOI
add DOI badge from Zenodo
Merge pull request #106 from lairdm/master
A test to ensure Bio::PrimarySeqI->trunc() doesn't use clone() for a Bio::Seq::RichSeq type object
Darn you, emacs, putting tab characters in. Sorry, didn't realize I hadn't changed my configs after reinstalling my laptop last month.
Merge branch 'master' of https://github.com/lairdm/bioperl-live
Added Bio::Seq::RichSeq as a seq object type that will cause Bio::PrimarySeqI->trunc() not to do a clone of the original object first. The clone was cloning features of the rich sequence object outside the requested range in trunc()
Remove cruft (soz)
Merge branch 'topic_105'
fix #105 - find the real "first orf"
Open Bio::DB::Taxonomy flatfile read-only
skip tests when using perl < 5.12
Run commits
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Recent Commits to bioperl-run:master

Merge pull request #15 from adsj/master
Supply TEMPLATE and SUFFIX for temporary query sequence files.
Raxml: use File::Spec->devnull() instead of our own code and do not import extra stuff into namespace
Merge pull request #13 from hettling/master
convert to markdown for consistency
convert to markdown for consistency
removed obsolete whitespace
StandAloneBlastPlus: Improved 'db_info' Algorithm ID regex,
Added MYMETA.json to .gitignore
Added -d option (random starting tree) to raxml run, because raxml
(1) when -w option was provided with a custom directory, 'run' always
WBCommandExts.t: Fixed a pending TODO related to
Update Build.PL, MYMETA.json with build dependencies
no dependencies on any of the Test::* or Sub::Uplevel in any test (except maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
Update Build.PL with config_requires and build_requires; add MANIFEST
Merge branch 'master' into topic/move_WrapperBase
fixed translate_params tests according to discussion at commit a6d0dc2; removed TODO around translate_params test
move StandAloneBlast* and WrapperBase* from root/Bio... to root/lib/Bio...
Merge branch 'master' of ../move_WrapperBase/bioperl-wb into topic/move_WrapperBase
test parameters independent of their order as issued on command line
Ext commits
RSS

Recent Commits to bioperl-ext:master

markdown-ize README
moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
Bioperl-DB (BioSQL)
RSS

Recent Commits to bioperl-db:master

Format
Update
Fix various Taxonomy values that are tested. Yes, this will break again.
Run perltidy on this, add some documentation
Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
add MANIFEST.SKIP
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
test commit to check SVN::Notify
Build.PL now checks for DBD drivers and attempts to DTRT
remove MANIFEST.SKIP
update Changes
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